Didn't Sean say at one point Pete tried to fire him, but John interceded, saying firing him for Petty Pete's personal reasons could create an HR issue for the company? And that's when Sean was given a job as a DUT agent? If that's the case, it's clear that John knew Pete was a liability, and chose to look the other way.
Because while "Pete's an owner and can't be fired," may technically be true, no one forced John to stay in business with him. John is a grown man, with a lot of financial privilege and resources. Would it have cost him money to get out of the partnership? Of course, but if he's the great businessman he wants everyone to think he is, he could have started another business or gotten another job.
The real question for me is, can you put a price tag on your integrity and personal moral values? Apparently, in John's case, you can. And that price is a couple of rental properties, luxury vacations, and some Louis Vuitton bags.